Purpose Dietary microorganisms are hypothesised to contribute to human health by modulating gut microbiota composition and function. However, evidence of their impact on health at the level of the overall diet is still emerging. In this study, we examined associations of dietary intake of live microorganisms, fermented foods, and microbial richness with cardiometabolic health. Methods We analysed baseline data of 440 adults (≥ 18 years) in the Swiss Kidney Stone Cohort (SKSC). Foods were categorised by live microorganism levels (low, < 104 CFU/g; medium [Med], 104–10⁷ CFU/g; or high [Hi], > 10⁷ CFU/g) and fermented food descriptors, including core microbiota. A microbial richness index was calculated based on the number of unique microbial species in fermented foods. Adjusted linear regression models assessed associations of MedHi food (> 104 CFU/g) intake, fermented food intake, and the fermented food microbial richness index with cardiometabolic parameters. Results Higher intake of microbe-rich MedHi foods was associated with lower diastolic blood pressure (β = − 1.99 × 10–2; CI − 3.71 × 10–2, − 2.82 × 10–3; p = 0.02), with fruit and vegetable consumption influencing this relationship. Total fermented food intake was not associated with any of the cardiometabolic parameters, but a higher value for the microbial richness index was associated with lower systolic blood pressure (β = − 2.07 × 10–3; CI − 3.85 × 10–3, − 2.95 × 10–4; p = 0.02) and glycated haemoglobin (β = − 1.22 × 10–5; CI − 2.14 × 10–5, − 3.11 × 10–6; p = 0.01), independent of any food subgroups. Conclusion Greater diversity of microbes from fermented foods was associated with lower systolic blood pressure and glycated haemoglobin in this study, suggesting potential cardiometabolic benefits.